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Biogeochemical cycles
of elements (nitrogen, sulfur, metals)
1
L.P. Wackett, A. G. Dodge, L. B. Ellis, 2004
Microbial Genomics and the Periodic Table,
Appl. Environ. Microbiol., 70, 647 - 655
The elements/metals of life www.webelements.com
Ca: 1.2 kg
K: 150 g
Na: 70 g
Mg: 20-30 g
Essential
Transition Metals
Fe: 4.5 g
Zn: 2.3 g
Cu: 0.072 g
Mo: 0.009 g
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
C: 17250 g
N: 1950 g
O: 45750 g
P: 825 g
S: 150 g
Se: 0.00375 g
2
References - Biogeochemical cycles of elements
A. Butler, 1998 Acquisition and Utilization of Transition Metal Ions by Marine Organisms, Science, 281, 207- 210
F. M. M. Morel and N. M. Price , 2003
Science , 300, 944-947, The Biogeochemical Cycles of Trace Metals in the Oceans
L.P. Wackett, A. G. Dodge, L. B. Ellis, 2004
Microbial Genomics and the Periodic Table, Appl. Environ. Microbiol., 70, 647 - 655
M. Rudolf, P.M.H. Kroneck, 2005 The nitrogen cycle: Its biology. Metal Ions in Biological Systems, 43, 75-103
B.B. Ward, D.G. Capone, J.P. Zehr, 2007 Oceanography 20,101–109, What's New in the Nitrogen Cycle ?
S.M. Sievert, R.P. Kiene, H.N. Schulz-Vogt, 2007 Oceanography 20, 117–123, The Sulfur Cycle
SCOR Working Group , 2007 GEOTRACES – An international study of the global marine biogeochemical cycles of trace elements
and their isotopes, Chemie der Erde, 67, 85–131
G. M. Gadd, 2010 Metals, minerals and microbes: geomicrobiology, and bioremediation, Microbiology, 156, 609–643
3
http://en.wikipedia.org/wiki/Sulfur_cycle
http://www.britannica.com/EBchecked/topic/65875/biogeochemical-cycle
S.M. Sievert, R.P. Kiene, and H.N. Schulz-Vogt, 2007
Oceanography 20, 117–123, The Sulfur Cycle
E.M. Cameron, 1982
Nature 296, 145-148, Sulfate and sulfate reduction in the early Precambrian oceans
G. Wächtershäuser, 1988
Syst Appl Microbiol, 10 , 207-210, Pyrite formation, the first energy source for life: a
hypothesis
R.K. Thauer, A. K. Kaster, et al., 2010
Annu Rev Biochem, 79, 507-36, Hydrogenases from methanogenic archaea, nickel, a novel
cofactor, and H2 storage
T. Urich et al., 2006
Science 311, 996 – 999, X-ray Structure of a Self-Compartmentalizing Sulfur Cycle
4
5
Citation Muhumuza Moses (Lead Author);C Michael Hogan (Topic Editor) "Biogeochemical cycles". In: Encyclopedia of Earth. Eds. Cutler J. Cleveland (Washington, D.C.: Environmental Information Coalition, National Council for Science and the Environment). Last revised Date December 24, 2011. <http://www.eoearth.org/article/Biogeochemical_cycles?topic=49553>
As the Earth is essentially a closed system
with respect to matter, we can say that all
matter on Earth cycles .
Estimated evolution of atmospheric O2
The red and green lines represent the range of the estimates: stage1: 3.85–2.45 Gyr (Ga),
stage2: 2.45–1.85Ga, stage3: 1.85–0.85Ga, stage4: 0.85–0.54Ga, stage5: 0.54Ga–present www.globalchange.umich.edu/globalchange1/current/lectures/Perry_Samson_lectures/evolution_atm/index.html
H.D. Holland, Phil. Trans. R. Soc. B (2006) 361, 903-915
Forms of Life – From Anaerobic to Aerobic
anoxic conditions (-O2) vs oxic conditions (+O2)
6
Today’s Energy Conservation: Reduction of O2 to H2O
Humans are Aerobes
7
G. Wächtershäuser
Munich/Chapel Hill
8
“The deep past of the Earth is
unobservable. Therefore, the
problem of the origin of life can
only be approached by a theory.”
Quote from Origin of Life: RNA World versus Autocatalytic Anabolist
See lecture by T. Cech, Nobel Prize in Chemistry, 1989
T. R. Cech
University of Colorado, Boulder
Emergence of life on the ocean floor hydrothermal vent, Russel and Hall, 1997
9
Basic Redox Couples Thauer et al., Bacteriol. Rev., 41, 100-180 (1977)
10
Biogeochemical Cycles
• Metabolism: All organisms transform (different) compounds
• Metabolic pathways constitute closed global cycles, otherwise intermediates
will accumulate. The larger the amount of the accumulated intermediate, the better
substrate it will be for organisms. On a geological time scale, a new metabolic
pathway will develop which will convert the intermediate.
A B
• Metabolic pathways can be organized and classified according to different
aspects, such as with regard to the ELEMENTS.
11
Elements in the Ocean
12
A. Butler, 1998
Acquisition and Utilization of Transition Metal Ions by
Marine Organisms, Science, 281, 207- 210
Essential Metal Sites (V, Fe, Cu, Mo)
13
A. Butler, 1998
Acquisition and Utilization of
Transition Metal Ions by Marine
Organisms, Science, 281,
207- 210
Vertical profiles of dissolved zinc and iron concentrations in the
north Pacific Ocean.
F M M Morel, N M Price Science 2003, 300 ,944-947 14
(A) Release of complexing agents and metal ligand complexes from marine plankton: CdX,
phytochelatin-Cd complex released by diatoms; CuY, peptide complexes of Cu released by
coccolithophorids; CuZ, unidentified Cu ligand complex released by Synechococcus; sid,
siderophore released by heterotrophic bacteria and cyanobacteria; L, unidentified Co
complexing agent released by Prochlorococcus; C, Cys; E, Glu; G, Gly; Q, Gln; and R, Arg.
F M M Morel, N M Price Science 2003,
300,44-947
15
The N cycle, illustrating the metal cofactors in each enzymatically
catalyzed step. (B) Primary metal requirements for C, N, and P
acquisition and assimilation by phytoplankton
F M M Morel, N M Price Science 2003,
300, 944-947 16
A Cadmium enzyme from a marine organism Lane et al., NATURE, 435, 42 (2005)
Active Cd-Carbonic Anhydrase
(purified by chromatography;
metal analysis by X-ray
spectroscopy)
Note: Until most recently, this
enzyme has been regarded as a
classical Zn-dependent enzyme.
And indeed, usually Cd is highly
toxic, replacing Zn in many
important proteins.
17
The Nitrogen Cycle: Note Activities of Microorganisms http://en.wikipedia.org/wiki/Nitrogen_cycle
18
Important Reactions and Metal Enzymes of the Nitrogen Cycle
19
Oxidation states of N
+5 +3 +2 +1 0 -1 -3
NO3- NO2
- NO N2O N2 H2NOH NH3
20
New intermediate: hydrazine, H2NNH2 Kuypers et al. (2003) „Anaerobic ammonium oxidation by anammox bacteria in the Black Sea”,
Nature 422, 608-611
Essential Metals of the N Cycle
Fe Cu Mo/V
- Nitrate Reductase - Nitrate Reductase
- Nitrite Reductase - Nitrite Reductase
- NO Reductase
- N2O Reductase
- Nitrogenase - Nitrogenase
- Ammonia Mono-
oxygenase
- Hydroxylamine
Oxidoreductase
21
22
Nitrate Reductase
NO3- + 2H+ + 2e- NO2
- + H2O
23
Mo bound to Molybdopterin (a dithiolene – coordinates both Mo and W)
JOURNAL of BIOLOGICAL CHEMISTRY (2009) 284, p. e10, N Kresge, R D Simoni, R L Hill:
The Discovery and Characterization of Molybdopterin - the Work of K. V. Rajagopalan)
24
PDB code: 2NAP
Numerous different forms of
nitrate reductase depending on
the organism
http://www.ebi.ac.uk/thornton-
srv/databases/cgi-
bin/enzymes/GetPage.pl?ec_nu
mber=1.7.99.4
25
Dissimilatory Nitrite Reductase
NO2- + 8H+ + 6e- NH4
+ + 2H2O
26
Cytochrome c Nitrite Reductase
Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, Kroneck
PMH (1999) Nature, 400 , 476–80
27
Nitrogen Uptake
• Nitrogen is an important constituent of biopolymers and numerous essential
biomolecules. The only N compound which can be taken up by higher organisms
is Ammonium, NH4+.
Amino acid synthesis: Amination of α-Ketoglutarate
(assimilatory process vs dissimilatory process)
28
Biological N2 Fixation
Microorganisms can do the job under „normal conditions“ (T, P)
• free living soil bacteria, e.g. Azotobacter vinelandii
• Cyanobacteria with specialized cells, e.g. Anabaena sp., Nostoc sp.)
• Rhizobia which live in special plant organelles (root noudles)
The process, however, is costly. Plants have to deliver up to 25% of their
photosynthetically produced ATP to N2 fixing bacteria in the root nodules.
Note: N2 Fixation is
an anaerobic process
29
N2 Fixation http://en.wikipedia.org/wiki/Nitrogenase
N2 + 8H+ + 16 Mg2+ATP + 8e-
2NH3 + H2 + 16 Mg2+ADP + 16 Pi 30
The chemical speciation of arsenic in the stratified water column of Mono Lake, California
(left) as explained by the metabolism of arsenic by microbial populations present in the
water column (right).
R S Oremland, J F Stolz Science 2003, 300:939-944 31
Phylogenetic diversity of representative arsenic-metabolizing prokaryotics.
R S Oremland, J F Stolz Science 2003, 300,939-944 32
33
The Biogeochemical Cycle of Sulfur
Life without Dioxygen – Respiration with S-Oxides
Reduction of SO42- to H2S
34 http://www.scienceclarified.com/Oi-Ph/Oxygen-Family.html
Reactions of the Biogeochemical Sulfur Cycle SO4
-2
Sulfate Reduction
(Assimilatory)
Organic Sulfur
H2S
Mineralization
Sulfur Oxidation
Sulfate Reduction
(Dissimilatory) Elemental Sulfur
Sulfur Oxidation
Sulfur Reduction
35
Oxidation/Reduction of Sulfur Compounds Coupled to
Energy Conservation Evolved Early in Prokaryotic Evolution
Bacteria Eucarya
Archaea
A. fulgidus
D.desulfuricans
D. vulgaris
T.denitrificans
36
S. Shima et al., Science (2008), 321, 572 - 575
Tracking Footprints of Early Life Nature’s Toolbox to handle Dihydrogen
H2 ⇄ 2H+ + 2e-
37
Overall structure of a Fe-only H2ase from (Handbook of Metalloproteins)
uni- vs bidirectional/
Ni,Fe vs Fe-only
H2 ⇄ 2H+ + 2e-
38
Presence of Toxic Ligands at Active Site
Analysis of CO and CN- by FT IR
39
Fe-only vs Ni,Fe Hydrogenase
Fe2
S
Fe1
S
(Cys)S
H2O
[4Fe4S]
O
C
N
C
O
CN
C
H-Cluster derFe-only Hydrogenase
(Cys)S Ni
(Cys)S(Cys)S
Fe(Cys)S
X
O
CN
C
N
C
[NiFe] Cluster derNi,Fe Hydrogenase
40
Life without O2 - Sulfur Respiration Reduction of SO4
2- to H2S, a multi-electron, multi-proton transfer
process coupled to energy conservation
41
SO42- must be first activated,
then microorganisms can eat it
APS ⇄ AMP + SO32-
Activation of sulfate (E°’ = -516 mV) to
adenosine-5’-phosphosulfate = APS (E°’ = -60 mV)
42
APS Reductase from thermophilic Archaeoglobus fulgidus Fritz et al., PNAS (2002), 99, 1836-41; Schiffer et al., Biochemistry (2006), 45, 2960-67
43
APSR has two [4Fe-4S] – Clusters which interact
9.8 A
310 320 330 340 350 360 370 380
Magnetic field [mT]
2.078 1.941 1.902 2.066 2.045 1.976 1.938 1.890
310 320 330 340 350 360 370 380
Magnetic field [mT]
I II I II
Eo‘ = - 60 mV Eo‘ = - 520 mV >>>
[+] [2+] [+] [+]
44
Chemistry of Sulfite Reduction
Sulfite reduced to
sulfide (directly or via
trithionate/thiosulfate)
by sulfite reductase in
a six-electron transfer
process
Dissimilatory (dSIR) Assimilatory (aSIR)
Sulfite Reduction
ATP PPi
APS
ATP ADP
2 [H]
6 [H]
2 [H]
6 [H]
AMP
3 H2O
PAPS
PAPS
3 H2O
SO32 SO3
2
S3O62
S2O32
S2
S2
ATP-Sulfurylase APS-Kinase
SO32
S2
SO42
45
SIR contains Siroheme
Siroheme = heme-type prosthetic group
catalyzes the six-electron reduction of sulfite to sulfide, and of nitrite to ammonia
formed by methylation, oxidation, and Fe insertion into uroporphyrinogen III
Siroheme
(green)
Heme b
(red)
46
Sulfite Reductase (36 Fe) from Archaeoglobus fulgidus
SO32- + 6e- + 8H+ → H2S + 3 H2O
Schiffer et al. (2008) J. Mol. Biol., 379, 1063-74; Parey et al. (2010) Biochemistry, 49, 8912-21
Unique cofactor: Siroheme coupled to [4Fe-4S]
40 60 80 100 120 140 160 180
g- Value
Magnetic Field [mT]
15.6 8.27 5.63 4.26 3.43 2.87 2.47 2.16 1.93 1.74
30 40 50 60 70 80 90
A B
Magnetic Field [mT]
g- Value
20.1 17.1 14.9 13.3 11.9 10.8 9.9 9.13 8.47 7.9
EPR (X-Band), resonances between g 18 and g 1.9
47
Overall structure of A. fulgidus dSIR 22 complex
• Final model contains four siroheme
and eight [4Fe-4S] centers = 36 Fe
• N- and C-terminal ends involved in
intradimer and interdimer
formation
• Tetrameric state may help to
survive in hot environments
• One -unit contains the catalytic
siroheme center
-subunit -subunit
β-subunit β-subunit
γ-subunit DrsC, interacts with
weakly with 22 complex in A.
Fulgidus, however strongly in D.
vulgaris 48
Cofactors of A. fulgidus dSIR
Functional and structural siroheme-[4Fe-4S] centers in one dimer; both sirohemes are
arranged towards each other.
Minimal distance between the acetate carboxylates 9.6 Å; distance 3.9-4.3 Å from the siroheme
to next [4Fe-4S] cluster.
49
Cofactors of Sulfite Reductase Schiffer et al., J. Mol. Biol. (2008), 379, 1063-74
• Catalytic (left) and structural siroheme-[4Fe-4S] center (right) in one
dimer: note the blocking tryptophan in the structural center
50
SO32- Adduct and the Substrate Channel
Positively charged residues guide the substrate Parey et al. (2010) Biochemistry 49, 8912-21
51
Reactivity in solution & in crystallo of A. fulgidus dSIR Parey et al. (2010) Biochemistry (2010) 49, 8912
52
Structure of a Self-Compartmentalizing Sulfur Cycle T. Urich et al. (2006) Science 311, 996 – 999
53